From 86cb4013f093ad3d923eab215b4bf5239e85ce44 Mon Sep 17 00:00:00 2001 From: Paulo Cesar Ventura <42674294+paulocv@users.noreply.github.com> Date: Mon, 26 Feb 2024 14:28:42 -0500 Subject: [PATCH 1/8] Add CEPH metadata file --- model-metadata/CEPH-Rtrend_rsv.yaml | 38 +++++++++++++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 model-metadata/CEPH-Rtrend_rsv.yaml diff --git a/model-metadata/CEPH-Rtrend_rsv.yaml b/model-metadata/CEPH-Rtrend_rsv.yaml new file mode 100644 index 00000000..571b39e9 --- /dev/null +++ b/model-metadata/CEPH-Rtrend_rsv.yaml @@ -0,0 +1,38 @@ +team_name: "CEPH Lab at Indiana University" +team_abbr: "CEPH" +model_name: "Rtrend RSV" +model_abbr: "Rtrend_rsv" +model_contributors: [ + { + "name": "Marco Ajelli", + "affiliation": "Indiana University Bloomington", + "email": "majelli@iu.edu", + }, + { + "name": "Paulo C. Ventura", + "affiliation": "Indiana University Bloomington", + "email": "pventura@iu.edu", + }, + { + "name": "Maria Litvinova", + "affiliation": "Indiana University Bloomington", + "email": "malitv@iu.edu", + }, + { + "name": "Allisandra G. Kummer", + "affiliation": "Indiana University Bloomington", + "email": "alkummer@iu.edu", + }, + { + "name": "Alessandro Vespignani", + "affiliation": "Northeastern University", + "email": "a.vespignani@northeastern.edu", + }, +] +license: "CC-BY-4.0" +data_inputs: "Weekly incident RSV hospitalizations from RSV-NET" +methods: "A renewal equation method based on Bayesian estimation of Rt from past hospitalization data." +methods_long: "Model forecasts are obtained by using a renewal equation based on the estimated net reproduction number Rt. We use a spline interpolation to obtain daily data from weekly incidence, then apply a lowpass filter to extract the main trend. We then use MCMC Metropolis-Hastings sampling to estimate the posterior distribution of Rt based on the filtered data, considering an informed prior on Rt based on RSV literature. The estimated Rt in the last weeks of available data is used to forecast Rt in the upcoming weeks, with a drift term proportional to the current incidence. Finally, we use the renewal equation with the posterior distribution and trend of the estimated Rt to forecast rSV hospitalization trajectories." +ensemble_of_models: false +ensemble_of_hub_models: false +website_url: https://publichealth.indiana.edu/research/faculty-directory/profile.html?user=majelli From f8507a954b760e48eccf0dc98c9cf4f02e8763df Mon Sep 17 00:00:00 2001 From: Paulo Cesar Ventura <42674294+paulocv@users.noreply.github.com> Date: Mon, 26 Feb 2024 15:27:48 -0500 Subject: [PATCH 2/8] CEPH_2024-02-25 --- model-output/2024-02-25_CEPH-Rtrend_rsv.parquet | Bin 0 -> 14200 bytes 1 file changed, 0 insertions(+), 0 deletions(-) create mode 100644 model-output/2024-02-25_CEPH-Rtrend_rsv.parquet diff --git a/model-output/2024-02-25_CEPH-Rtrend_rsv.parquet b/model-output/2024-02-25_CEPH-Rtrend_rsv.parquet new file mode 100644 index 0000000000000000000000000000000000000000..dc9ef2756d43852ed549183394568b803f544a49 GIT binary patch literal 14200 zcmch82Ut_t*60Zm4CM$2!HB4#HzNrUnkXxwg(?IH5NZlNp?6UbQLrI)1q)b4#0FLz z8wx0*B6jT9v11)OZwGM3xjOfK|9kiT`Eqv7Uc0Qm);^qtAB)Q%%aciD6>qW}85@pa z@+xc}3?pM?Ewc7Fa@TOO8d-s?phJ_o> zWU65bBPq%$=?QTO$x&iKW(-+Qt82K{GJ@6`f)U+_^zXJDISvtpk>zA`sG%Q3kUW_} z*7;7P$~Y2&B_xZe@hKUpKM`w#nUKB@QvSUAiO>&2bjT`$geqhT(&J(>2WVVF(E5#F zG-rs>c{!bb*z1=R0@>Od$xh}swOWVat>OZq-Wk+IeP zK{EaY6bW1o&!XM5ARy9m+2d`~%uwa=VH^E+Kf6wfp(?)s*pRZA(<9|h*7mZlrH!l&3P5s+BuD=s79@GOpa6;--3Eead)_0>*q!MM+(->CtUs)Wne}ppdgC_pnDLV1L z$Wau;#YDxWr(~rLC}kc&YYD;Vg^JNZ6&XE$-{_ZA{p1R1S%T!u1WC-V2qS$Tr2KjJ z6M5xof03u0l9id7l^KQwRzw2UjH{7OI$`Lp6Q__aIK`s7%Q#i#s?(X%1Oj#gH^I7b z3U&vlWA|_>b|1IH9wJx|x*ntJDY~Aa>jh3Rc%(^`jgvJm#&c;i%<`C0yaoZmqdf9=Y z{BVLXu2w{aJA~>dbyO|bNbsJ&G~5a<$J>b2TgHK~s=+*kXov$g2DhWyf>BjOM<~k@ zx9c&2YgM5SSI&2Unhq0Xd@&Phty5IT7%^bPs%_3Y{3n8r+*|ji`*xro@8Eqd#~MsK ziu~>>0fZ3isS{vL6>)aSNn6~`gau3GR>?h;OoC`)Ey8i!dgNh~GB#dc1i(9Mpzm{g zB8)oQ*=jp#0=QHSohn}M45fs1x8{6e;q@>HjuGBZs6Olh591!bIIs)BNN%tW?c@sg zt(zrQPn_|hYIo=(c&^-2><&#G=l73z=LS^fh<46)Hwb4Y8Aqmjz?TlA5w!gtcrNCJ zH&MO7{%n3Gd#X3yOZ9RN%XTc2$AkA8*gSGlvJ4@)Ay|C31lgzhM1klOT}B-@~3g z3x*ThZXA2z90mr4(bPb=)lm?y7aW3@VG*>DCIP&saA*xLg28Z=T-9#5NI0{*Ibln; 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We use a spline interpolation to obtain daily data from weekly incidence, then apply a lowpass filter to extract the main trend. We then use MCMC Metropolis-Hastings sampling to estimate the posterior distribution of Rt based on the filtered data, considering an informed prior on Rt based on RSV literature. The estimated Rt in the last weeks of available data is used to forecast Rt in the upcoming weeks, with a drift term proportional to the current incidence. Finally, we use the renewal equation with the posterior distribution and trend of the estimated Rt to forecast rSV hospitalization trajectories." +methods_long: "Model forecasts are obtained by using a renewal equation based on the estimated net reproduction number Rt. We use a spline interpolation to obtain daily data from weekly incidence, then apply a lowpass filter to extract the main trend. We then use MCMC Metropolis-Hastings sampling to estimate the posterior distribution of Rt based on the filtered data, considering an informed prior on Rt based on RSV literature. The estimated Rt in the last weeks of available data is used to forecast Rt in the upcoming weeks, with a drift term proportional to the current incidence. Finally, we use the renewal equation with the posterior distribution and trend of the estimated Rt to forecast RSV hospitalization trajectories." ensemble_of_models: false ensemble_of_hub_models: false website_url: https://publichealth.indiana.edu/research/faculty-directory/profile.html?user=majelli From 9fb0abe4558d39ac82a2d5504c7fad980fd749cc Mon Sep 17 00:00:00 2001 From: Paulo Cesar Ventura <42674294+paulocv@users.noreply.github.com> Date: Tue, 27 Feb 2024 09:26:14 -0500 Subject: [PATCH 5/8] Update metadata for missing fields Adds `schema_version` and `model_version` to the metadata file. --- model-metadata/CEPH-Rtrend_rsv.yaml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/model-metadata/CEPH-Rtrend_rsv.yaml b/model-metadata/CEPH-Rtrend_rsv.yaml index 1a856f53..447996d1 100644 --- a/model-metadata/CEPH-Rtrend_rsv.yaml +++ b/model-metadata/CEPH-Rtrend_rsv.yaml @@ -1,7 +1,9 @@ +schema_version: "https://raw.githubusercontent.com/Infectious-Disease-Modeling-Hubs/schemas/main/v2.0.0/admin-schema.json" team_name: "CEPH Lab at Indiana University" team_abbr: "CEPH" model_name: "Rtrend RSV" model_abbr: "Rtrend_rsv" +model_version: 2024-01-08 model_contributors: [ { "name": "Marco Ajelli", From 279ce87c34d65767a08aff9da2b304cc540ea76e Mon Sep 17 00:00:00 2001 From: Paulo Cesar Ventura <42674294+paulocv@users.noreply.github.com> Date: Tue, 27 Feb 2024 16:53:08 -0500 Subject: [PATCH 6/8] Add horizon = 4 --- .../2024-02-25_CEPH-Rtrend_rsv.parquet | Bin 0 -> 16175 bytes 1 file changed, 0 insertions(+), 0 deletions(-) create mode 100644 model-output/CEPH-Rtrend_rsv/2024-02-25_CEPH-Rtrend_rsv.parquet diff --git a/model-output/CEPH-Rtrend_rsv/2024-02-25_CEPH-Rtrend_rsv.parquet b/model-output/CEPH-Rtrend_rsv/2024-02-25_CEPH-Rtrend_rsv.parquet new file mode 100644 index 0000000000000000000000000000000000000000..e0e5b9554bd7e0c41ebbdad17557947739e767e7 GIT binary patch literal 16175 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